I was forced to run a stand-alone cooler (no factory heat exchanger. Went from an ~15K BTU stacked plate cooler to a 30K BTU unit) for some time.
In the winter, it would take the trans a good little bit to try to come up to temp. This bothered me (I'd struggle to reach 125*F during an entire drive in the morning when ambient temps were below 40*F). I didnt like to bang on the trans when the fluid was that cool. This was in 3rd at 2400 RPM. The ambient air flow simply kept things on the very cool side.
My goal would be to have trans outlet temps never exceed 165*F, while keeping the factory heat exchanger. If your operating temps are higher than desired, then ditch the heat exchanger or get a bigger cooler.
You will now have your cooler closer to the radiator (thus fan), with less impediment to pull air through the cooler. Its performance should only increase. I'd try keeping the exchanger and see how it does. You can bypass it later if needed.
Just MHO James. I know that a lot of folks run stacked plate coolers with no exchanger and they dont worry about it.